GENE REFERENCE / HGNC:11204

SOX9

SRY-box transcription factor 9

protein-coding gene17q24.3Gene information

What does this gene do?

The SOX9 gene provides instructions for making a protein that plays a critical role during embryonic development. The SOX9 protein is especially important for development of the skeleton and plays a key role in the determination of sex before birth. The SOX9 protein attaches (binds) to specific regions of DNA and regulates the activity of other genes, particularly those that control skeletal development and sex determination. On the basis of this action, the SOX9 protein is called a transcription factor.

Source: MedlinePlus, National Library of Medicine. Source publication: 2022-06-28. Source review: 2016-12.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
isolated Pierre-Robin syndromeMONDO:0009869 · Evaluated 2024-08-06	Autosomal dominant	LimitedSkeletal Disorders Gene Curation Expert Panel
Cooks syndromeMONDO:0007134 · Evaluated 2020-09-16	Autosomal dominant	LimitedSkeletal Disorders Gene Curation Expert Panel
campomelic dysplasiaMONDO:0007251 · Evaluated 2020-06-01	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 589
Submissions for variants in or overlapping this gene: 813
Submissions explicitly reporting this gene: 766
Alleles reported pathogenic / likely pathogenic: 162
VariationIDs with uncertain significance: 208
VariationIDs with conflicting classifications: 25

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about SOX9?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 162 alleles in SOX9 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in SOX9.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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